AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene028406

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene028406.t1 MTR_4g094325 97.183 213 6 0 1 213 27 239 1.69e-151 420
MS.gene028406.t1 MTR_1g099010 62.802 207 73 2 7 213 15 217 8.81e-86 253
MS.gene028406.t1 MTR_4g094332 63.679 212 73 2 6 213 13 224 5.39e-84 248
MS.gene028406.t1 MTR_4g094328 62.212 217 77 2 2 213 8 224 5.75e-84 248
MS.gene028406.t1 MTR_4g094330 62.212 217 77 2 2 213 8 224 5.75e-84 248
MS.gene028406.t1 MTR_6g034975 61.215 214 75 3 4 213 1 210 6.82e-78 233
MS.gene028406.t1 MTR_0119s0010 59.898 197 69 2 14 210 23 209 8.38e-69 209
MS.gene028406.t1 MTR_0119s0020 59.898 197 69 2 14 210 23 209 8.38e-69 209
MS.gene028406.t1 MTR_2g008110 59.898 197 69 2 14 210 23 209 1.03e-68 209
MS.gene028406.t1 MTR_4g094335 55.238 210 87 2 10 212 20 229 3.04e-66 204
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene028406.t1 AT3G43660 58.852 209 73 3 6 213 2 198 1.43e-81 241
MS.gene028406.t1 AT1G21140 59.524 210 71 5 6 213 3 200 4.41e-74 223
MS.gene028406.t1 AT3G43630 61.053 190 69 1 23 212 12 196 1.31e-71 216
MS.gene028406.t1 AT1G76800 59.794 194 72 1 20 213 9 196 2.36e-69 211
MS.gene028406.t1 AT3G25190 57.209 215 83 3 8 213 3 217 5.06e-69 210

Find 43 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATTAACTTCATTGTTATTA+TGG 0.164844 4.2:-18632130 None:intergenic
ATGGCTATGGCTATTACTTT+TGG 0.286846 4.2:+18632698 MS.gene028406:CDS
GGTGCAACTGTTCCATTGTT+AGG 0.312326 4.2:+18632527 MS.gene028406:CDS
TCAATAACATCACTGATATT+AGG 0.320977 4.2:+18632266 MS.gene028406:CDS
ATGCTTCTAGCTGGATTTGC+AGG 0.330228 4.2:+18632320 MS.gene028406:CDS
TGAACTATAGCCAACTAATT+TGG 0.332042 4.2:-18632726 None:intergenic
TGGCTAAGGGCTGCTTTGTT+AGG 0.335118 4.2:+18632224 MS.gene028406:CDS
TTTCTTCGGTTTCTTGAGTT+TGG 0.348710 4.2:-18632172 None:intergenic
AATTGCAGGAGCATGTAGTA+TGG 0.371115 4.2:+18632346 MS.gene028406:CDS
CAACAAACAACCTTATCTTA+TGG 0.372163 4.2:-18632568 None:intergenic
ATAGCAGCTTGAAAAGGATT+TGG 0.379593 4.2:-18632479 None:intergenic
TATTGATACCAAACCATCAT+TGG 0.397645 4.2:-18632249 None:intergenic
GGATTTGCAGGACTAATTGC+AGG 0.405837 4.2:+18632332 MS.gene028406:CDS
GTTAGGAGCCAATGATGGTT+TGG 0.408839 4.2:+18632241 MS.gene028406:CDS
GGAGCATGTAGTATGGGAAT+TGG 0.413287 4.2:+18632353 MS.gene028406:CDS
ATAAGGTTGTTTGTTGTTGT+TGG 0.419241 4.2:+18632575 MS.gene028406:CDS
GTTGTTTGTTGTTGTTGGTA+TGG 0.425598 4.2:+18632580 MS.gene028406:CDS
TTGTTGGTGTTTGGTGGAGT+TGG 0.434863 4.2:+18632614 MS.gene028406:CDS
GTACACTCAATTTGACATAA+TGG 0.442870 4.2:+18632391 MS.gene028406:CDS
AGTGGTGGTTGGAGGTTGGA+TGG 0.447165 4.2:+18632679 MS.gene028406:CDS
TTAGAGTGGTGGTTGGAGGT+TGG 0.453273 4.2:+18632675 MS.gene028406:CDS
TTGTACTTTATGGTTTCTCT+TGG 0.457022 4.2:+18632104 None:intergenic
TTTGGCTTGACCAAATTAGT+TGG 0.462254 4.2:+18632716 MS.gene028406:CDS
GGTGGAGTTGGAGCAATACT+TGG 0.463894 4.2:+18632626 MS.gene028406:CDS
TGTGTTAGAGTGGTGGTTGG+AGG 0.467615 4.2:+18632671 MS.gene028406:CDS
TGTTAGGAGCAGCATTGGTA+AGG 0.467798 4.2:+18632543 MS.gene028406:CDS
TCAAAAGAGCACAATGGCTA+AGG 0.471142 4.2:+18632210 MS.gene028406:CDS
TTTGCATTGTTGGTGTTTGG+TGG 0.472445 4.2:+18632608 MS.gene028406:CDS
GGTTGGAGGTTGGATGGCTA+TGG 0.474740 4.2:+18632685 MS.gene028406:CDS
TCCATTGTTAGGAGCAGCAT+TGG 0.480068 4.2:+18632538 MS.gene028406:CDS
ATCAAAACAATGCTTCTAGC+TGG 0.493445 4.2:+18632311 MS.gene028406:CDS
TCTTGTGTTAGAGTGGTGGT+TGG 0.541101 4.2:+18632668 MS.gene028406:CDS
GCTTTGTTAGGAGCCAATGA+TGG 0.544587 4.2:+18632236 MS.gene028406:CDS
GATGCAATAGCAGCTTGAAA+AGG 0.549841 4.2:-18632485 None:intergenic
ACCAATGCTGCTCCTAACAA+TGG 0.557852 4.2:-18632539 None:intergenic
CAAAAGAGCACAATGGCTAA+GGG 0.565247 4.2:+18632211 MS.gene028406:CDS
GTTAGGAGCAGCATTGGTAA+GGG 0.568514 4.2:+18632544 MS.gene028406:CDS
ATTGCAGGAGCATGTAGTAT+GGG 0.575864 4.2:+18632347 MS.gene028406:CDS
ACATCACTGATATTAGGTGT+TGG 0.581679 4.2:+18632272 MS.gene028406:CDS
TGGTAAGGGACCATAAGATA+AGG 0.588888 4.2:+18632558 MS.gene028406:CDS
AATGTCTTGTGTTAGAGTGG+TGG 0.635471 4.2:+18632664 MS.gene028406:CDS
GAAAATGTCTTGTGTTAGAG+TGG 0.645932 4.2:+18632661 MS.gene028406:CDS
ACTATTTCAAAAGAGCACAA+TGG 0.670557 4.2:+18632204 MS.gene028406:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CATTAACTTCATTGTTATTA+TGG - chr4.2:18632133-18632152 None:intergenic 20.0%
! TCAATAACATCACTGATATT+AGG + chr4.2:18632266-18632285 MS.gene028406:CDS 25.0%
!!! ATAGTCAATGTTGTTTTCTT+CGG - chr4.2:18632189-18632208 None:intergenic 25.0%
CAACAAACAACCTTATCTTA+TGG - chr4.2:18632571-18632590 None:intergenic 30.0%
GTACACTCAATTTGACATAA+TGG + chr4.2:18632391-18632410 MS.gene028406:CDS 30.0%
TATTGATACCAAACCATCAT+TGG - chr4.2:18632252-18632271 None:intergenic 30.0%
TGAACTATAGCCAACTAATT+TGG - chr4.2:18632729-18632748 None:intergenic 30.0%
! ACTATTTCAAAAGAGCACAA+TGG + chr4.2:18632204-18632223 MS.gene028406:CDS 30.0%
! TCAGCAATTGCATTTTCATT+TGG + chr4.2:18632506-18632525 MS.gene028406:CDS 30.0%
!! ATAAGGTTGTTTGTTGTTGT+TGG + chr4.2:18632575-18632594 MS.gene028406:CDS 30.0%
ACATCACTGATATTAGGTGT+TGG + chr4.2:18632272-18632291 MS.gene028406:CDS 35.0%
ATAGCAGCTTGAAAAGGATT+TGG - chr4.2:18632482-18632501 None:intergenic 35.0%
ATCAAAACAATGCTTCTAGC+TGG + chr4.2:18632311-18632330 MS.gene028406:CDS 35.0%
GAAAATGTCTTGTGTTAGAG+TGG + chr4.2:18632661-18632680 MS.gene028406:CDS 35.0%
TTTCTTCGGTTTCTTGAGTT+TGG - chr4.2:18632175-18632194 None:intergenic 35.0%
! ATGGCTATGGCTATTACTTT+TGG + chr4.2:18632698-18632717 MS.gene028406:CDS 35.0%
!! AGTTTTGCATTGTTGGTGTT+TGG + chr4.2:18632605-18632624 MS.gene028406:CDS 35.0%
!! GTTGTTTGTTGTTGTTGGTA+TGG + chr4.2:18632580-18632599 MS.gene028406:CDS 35.0%
!! TTTGGCTTGACCAAATTAGT+TGG + chr4.2:18632716-18632735 MS.gene028406:CDS 35.0%
!!! TATGGCTAGTTTTGCATTGT+TGG + chr4.2:18632598-18632617 MS.gene028406:CDS 35.0%
AATGTCTTGTGTTAGAGTGG+TGG + chr4.2:18632664-18632683 MS.gene028406:CDS 40.0%
GATGCAATAGCAGCTTGAAA+AGG - chr4.2:18632488-18632507 None:intergenic 40.0%
TGGTAAGGGACCATAAGATA+AGG + chr4.2:18632558-18632577 MS.gene028406:CDS 40.0%
! AATTGCAGGAGCATGTAGTA+TGG + chr4.2:18632346-18632365 MS.gene028406:CDS 40.0%
! ATTGCAGGAGCATGTAGTAT+GGG + chr4.2:18632347-18632366 MS.gene028406:CDS 40.0%
! CAAAAGAGCACAATGGCTAA+GGG + chr4.2:18632211-18632230 MS.gene028406:CDS 40.0%
! CAACAGCACTTTTGTTGAAG+AGG + chr4.2:18632442-18632461 MS.gene028406:CDS 40.0%
! TCAAAAGAGCACAATGGCTA+AGG + chr4.2:18632210-18632229 MS.gene028406:CDS 40.0%
! TTTGCATTGTTGGTGTTTGG+TGG + chr4.2:18632608-18632627 MS.gene028406:CDS 40.0%
ACCAATGCTGCTCCTAACAA+TGG - chr4.2:18632542-18632561 None:intergenic 45.0%
GGAGCATGTAGTATGGGAAT+TGG + chr4.2:18632353-18632372 MS.gene028406:CDS 45.0%
GGATTTGCAGGACTAATTGC+AGG + chr4.2:18632332-18632351 MS.gene028406:CDS 45.0%
GGTGCAACTGTTCCATTGTT+AGG + chr4.2:18632527-18632546 MS.gene028406:CDS 45.0%
GTTAGGAGCCAATGATGGTT+TGG + chr4.2:18632241-18632260 MS.gene028406:CDS 45.0%
TCCATTGTTAGGAGCAGCAT+TGG + chr4.2:18632538-18632557 MS.gene028406:CDS 45.0%
TCTTGTGTTAGAGTGGTGGT+TGG + chr4.2:18632668-18632687 MS.gene028406:CDS 45.0%
! ATGCTTCTAGCTGGATTTGC+AGG + chr4.2:18632320-18632339 MS.gene028406:CDS 45.0%
! GCTTTGTTAGGAGCCAATGA+TGG + chr4.2:18632236-18632255 MS.gene028406:CDS 45.0%
! TTGTTGGTGTTTGGTGGAGT+TGG + chr4.2:18632614-18632633 MS.gene028406:CDS 45.0%
!! GTTAGGAGCAGCATTGGTAA+GGG + chr4.2:18632544-18632563 MS.gene028406:CDS 45.0%
!! TGTTAGGAGCAGCATTGGTA+AGG + chr4.2:18632543-18632562 MS.gene028406:CDS 45.0%
GGTGGAGTTGGAGCAATACT+TGG + chr4.2:18632626-18632645 MS.gene028406:CDS 50.0%
TGTGTTAGAGTGGTGGTTGG+AGG + chr4.2:18632671-18632690 MS.gene028406:CDS 50.0%
TTAGAGTGGTGGTTGGAGGT+TGG + chr4.2:18632675-18632694 MS.gene028406:CDS 50.0%
! TGGCTAAGGGCTGCTTTGTT+AGG + chr4.2:18632224-18632243 MS.gene028406:CDS 50.0%
AGTGGTGGTTGGAGGTTGGA+TGG + chr4.2:18632679-18632698 MS.gene028406:CDS 55.0%
GGTTGGAGGTTGGATGGCTA+TGG + chr4.2:18632685-18632704 MS.gene028406:CDS 55.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 18632113 18632754 18632113 ID=MS.gene028406
chr4.2 mRNA 18632113 18632754 18632113 ID=MS.gene028406.t1;Parent=MS.gene028406
chr4.2 exon 18632113 18632754 18632113 ID=MS.gene028406.t1.exon1;Parent=MS.gene028406.t1
chr4.2 CDS 18632113 18632754 18632113 ID=cds.MS.gene028406.t1;Parent=MS.gene028406.t1
Gene Sequence

>MS.gene028406

ATGGTTTCTCTTGGTAACCATAATAACAATGAAGTTAATGACATAGAAGCAAAGCAAAACCAAACTCAAGAAACCGAAGAAAACAACATTGACTATTTCAAAAGAGCACAATGGCTAAGGGCTGCTTTGTTAGGAGCCAATGATGGTTTGGTATCAATAACATCACTGATATTAGGTGTTGGAGCTGTGCATGAAGACATCAAAACAATGCTTCTAGCTGGATTTGCAGGACTAATTGCAGGAGCATGTAGTATGGGAATTGGAGAGTTTGTATCAGTGTACACTCAATTTGACATAATGGTAGCTCAAATGAAAAGAGAGAACAAAATCAACAGCACTTTTGTTGAAGAGGAAAAGAAGCTACTACCAAATCCTTTTCAAGCTGCTATTGCATCAGCAATTGCATTTTCATTTGGTGCAACTGTTCCATTGTTAGGAGCAGCATTGGTAAGGGACCATAAGATAAGGTTGTTTGTTGTTGTTGGTATGGCTAGTTTTGCATTGTTGGTGTTTGGTGGAGTTGGAGCAATACTTGGTAAAACATCAGTGAAAATGTCTTGTGTTAGAGTGGTGGTTGGAGGTTGGATGGCTATGGCTATTACTTTTGGCTTGACCAAATTAGTTGGCTATAGTTCACTTTGA
Protein sequence

>MS.gene028406.t1

MVSLGNHNNNEVNDIEAKQNQTQETEENNIDYFKRAQWLRAALLGANDGLVSITSLILGVGAVHEDIKTMLLAGFAGLIAGACSMGIGEFVSVYTQFDIMVAQMKRENKINSTFVEEEKKLLPNPFQAAIASAIAFSFGATVPLLGAALVRDHKIRLFVVVGMASFALLVFGGVGAILGKTSVKMSCVRVVVGGWMAMAITFGLTKLVGYSSL